PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences
items: Nomograms predict survival outcome of Klatskin tumors patients
items: No island-effect on glucocorticoid levels for a rodent from a near-shore archipelago
items: Effectiveness of slightly acidic electrolyzed water on bacteria reduction: in vitro and spray evaluation
items: Fasciola gigantica, F. hepatica and Fasciola intermediate forms: geometric morphometrics and an artificial neural network to help morphological identification
items: Injuries among adolescents in Greenland: behavioural and socio-economic correlates among a nationally representative sample
items: Co-expression network analysis reveals the pivotal role of mitochondrial dysfunction and interferon signature in juvenile dermatomyositis
items: Association between 9-minute walk/run test and obesity among children and adolescents: evidence for criterion-referenced cut-points
items: Molecular phylogeny and intraspecific differentiation of the Trapelus agilis species complex in Iran (Squamata: Agamidae) inferred from mitochondrial DNA sequences
items: Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences
type: item
type: AcademicArticle
description: Background The concept of chromatin domains attached to the nuclear matrix is being revisited, with nucleus described as a set of topologically associating domains. The significance of the tightly bound to DNA proteins (TBP), a protein group that remains attached to DNA after its deproteinization should be also revisited, as the existence of these interactions is in good agreement with the concept of the topologically associating domain. The work aimed to characterize the DNA component of TBP isolated from barley seedlings. Methods The tight DNA-protein complexes from the first leaves, coleoptiles, and roots of barley seedlings were isolated by purification with chromatography on nitrocellulose or exhaustive digestion of DNA with DNase I. Cloning and transformation were performed using pMOSBBlue Blunt Ended Cloning Kit. Inserts were amplified by PCR, and sequencing was performed on the MegaBace 1000 Sequencing System. The BLAST search was performed using sequence databases at NCBI, CR-EST, and TREP and Ensembl Plants databases. Comparison to MAR/SAR sequences was performed using http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/smar.cgi database. The prediction of G quadruplexes (GQ) was performed with the aid of R-studio library pqsfinder. CD spectra were recorded on a Chirascan CS/3D spectrometer. Results Although the barley genome is AT-rich (43% of GC pairs), most DNA fragments associated with TBP were GC-rich (up to 70% in some fractions). Both fractionation procedures yielded a high proportion of CT-motif sequences presented predominantly by the 16-bp CC(TCTCCC)2 TC fragment present in clones derived from the TBP-bound DNA and absent in free DNA. BLAST analysis revealed alignment with different barley repeats. Some clones, however, aligned with both nuclear and chloroplast structural genes. Alignments with MAR/SAR motifs were very few. The analysis produced by the pqsfinder program revealed numerous potential quadruplex-forming sites in the TBP-bound…
format: application/pdf
format: text/html
creator: Tatjana Sjakste
creator: Elina Leonova
creator: Rudolfs Petrovs
creator: Ilva Trapina
creator: Marion S. Röder
creator: Nikolajs Sjakste
subject: Cell Biology
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.8569
publisher: PeerJ Inc.
rights: © 2020 Sjakste et al.
abstract: Background The concept of chromatin domains attached to the nuclear matrix is being revisited, with nucleus described as a set of topologically associating domains. The significance of the tightly bound to DNA proteins (TBP), a protein group that remains attached to DNA after its deproteinization should be also revisited, as the existence of these interactions is in good agreement with the concept of the topologically associating domain. The work aimed to characterize the DNA component of TBP isolated from barley seedlings. Methods The tight DNA-protein complexes from the first leaves, coleoptiles, and roots of barley seedlings were isolated by purification with chromatography on nitrocellulose or exhaustive digestion of DNA with DNase I. Cloning and transformation were performed using pMOSBBlue Blunt Ended Cloning Kit. Inserts were amplified by PCR, and sequencing was performed on the MegaBace 1000 Sequencing System. The BLAST search was performed using sequence databases at NCBI, CR-EST, and TREP and Ensembl Plants databases. Comparison to MAR/SAR sequences was performed using http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/smar.cgi database. The prediction of G quadruplexes (GQ) was performed with the aid of R-studio library pqsfinder. CD spectra were recorded on a Chirascan CS/3D spectrometer. Results Although the barley genome is AT-rich (43% of GC pairs), most DNA fragments associated with TBP were GC-rich (up to 70% in some fractions). Both fractionation procedures yielded a high proportion of CT-motif sequences presented predominantly by the 16-bp CC(TCTCCC)2 TC fragment present in clones derived from the TBP-bound DNA and absent in free DNA. BLAST analysis revealed alignment with different barley repeats. Some clones, however, aligned with both nuclear and chloroplast structural genes. Alignments with MAR/SAR motifs were very few. The analysis produced by the pqsfinder program revealed numerous potential quadruplex-forming sites in the TBP-bound…
bibliographic citation: Sjakste et al. (2020) Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences. PeerJ 8:e8569 https://doi.org/10.7717/peerj.8569
date submitted: 2019-11-14
date accepted: 2020-01-15
issued: 2020-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sjakste
  given name: Tatjana
author list: Agent
  family name: Leonova
  given name: Elina
author list: Agent
  family name: Petrovs
  given name: Rudolfs
author list: Agent
  family name: Trapina
  given name: Ilva
author list: Agent
  family name: Röder
  given name: Marion S.
author list: Agent
  family name: Sjakste
  given name: Nikolajs
doi: 10.7717/peerj.8569
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-18
copyright: ©2020 Sjakste et al.
attribution name: Sjakste et al.

Nomograms predict survival outcome of Klatskin tumors patients
type: item
type: AcademicArticle
description: Objective Klatskin tumors are rare, malignant tumors of the biliary system with a poor prognosis for patient survival. The current understanding of these tumors is limited to a small number of case reports or case series; therefore, we examined prognostic factors of this disease. Methods A population cohort study was conducted in patients selected from the Surveillance, Epidemiology, and End Results (SEER) database with a Klatskin tumor that was histologically diagnosed between 2004 to 2014. Propensity-matching (PSM) analysis was performed to determine the overall survival (OS) among those with a Klatskin tumor (KCC), intrahepatic cholangiocarcinoma (ICCA), or hepatocellular carcinoma (HCC). The nomogram was based on 317 eligible Klatskin tumor patients and its predictive accuracy and discriminatory ability were determined using the concordance index (C-index). Results Kaplan-Meier analysis showed that patients with Klatskin tumors had significantly worse overall survival rates (1-year OS = 26.2%, 2-year OS = 10.7%, 3-year OS = 3.4%) than those with intrahepatic cholangiocarcinoma (1-year OS = 62.2%, 2-year OS = 36.4%, 3-year OS = 19.1%, p < 0.001) or hepatocellular carcinoma (1-year OS = 72.4% , 2-year OS = 48.5%, 3-year OS = 36.2%, p < 0.001). A poor prognosis was also significantly associated with older age, higher grade, SEER historic stage, and lymph node metastasis. Local destruction of the tumor (HR = 0.635, 95% CI [0.421–0.956], p = 0.03) and surgery (HR = 0.434, 95% [CI 0.328–0.574], p < 0.001) were independent protective factors. Multivariate Cox analysis showed that older age, SEER historic stage, and lymph node metastases (HR = 1.468, 95% CI [1.008–2.139], p = 0.046) were independent prognostic factors of poor survival rates in Klatskin tumor patients, while cancer-directed surgery was an independent protective factor (HR = 0.555, 95% CI [0.316–0.977], p = 0.041). The prognostic and protective factors were included in the nomogram (C-index for survival =…
format: application/pdf
format: text/html
creator: Feng Qi
creator: Bin Zhou
creator: Jinglin Xia
subject: Bioinformatics
subject: Diabetes and Endocrinology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Data Science
description: doi:10.7717/peerj.8570
publisher: PeerJ Inc.
rights: © 2020 Qi et al.
abstract: Objective Klatskin tumors are rare, malignant tumors of the biliary system with a poor prognosis for patient survival. The current understanding of these tumors is limited to a small number of case reports or case series; therefore, we examined prognostic factors of this disease. Methods A population cohort study was conducted in patients selected from the Surveillance, Epidemiology, and End Results (SEER) database with a Klatskin tumor that was histologically diagnosed between 2004 to 2014. Propensity-matching (PSM) analysis was performed to determine the overall survival (OS) among those with a Klatskin tumor (KCC), intrahepatic cholangiocarcinoma (ICCA), or hepatocellular carcinoma (HCC). The nomogram was based on 317 eligible Klatskin tumor patients and its predictive accuracy and discriminatory ability were determined using the concordance index (C-index). Results Kaplan-Meier analysis showed that patients with Klatskin tumors had significantly worse overall survival rates (1-year OS = 26.2%, 2-year OS = 10.7%, 3-year OS = 3.4%) than those with intrahepatic cholangiocarcinoma (1-year OS = 62.2%, 2-year OS = 36.4%, 3-year OS = 19.1%, p < 0.001) or hepatocellular carcinoma (1-year OS = 72.4% , 2-year OS = 48.5%, 3-year OS = 36.2%, p < 0.001). A poor prognosis was also significantly associated with older age, higher grade, SEER historic stage, and lymph node metastasis. Local destruction of the tumor (HR = 0.635, 95% CI [0.421–0.956], p = 0.03) and surgery (HR = 0.434, 95% [CI 0.328–0.574], p < 0.001) were independent protective factors. Multivariate Cox analysis showed that older age, SEER historic stage, and lymph node metastases (HR = 1.468, 95% CI [1.008–2.139], p = 0.046) were independent prognostic factors of poor survival rates in Klatskin tumor patients, while cancer-directed surgery was an independent protective factor (HR = 0.555, 95% CI [0.316–0.977], p = 0.041). The prognostic and protective factors were included in the nomogram (C-index for survival =…
bibliographic citation: Qi et al. (2020) Nomograms predict survival outcome of Klatskin tumors patients. PeerJ 8:e8570 https://doi.org/10.7717/peerj.8570
date submitted: 2019-10-11
date accepted: 2020-01-15
issued: 2020-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qi
  given name: Feng
author list: Agent
  family name: Zhou
  given name: Bin
author list: Agent
  family name: Xia
  given name: Jinglin
doi: 10.7717/peerj.8570
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-18
copyright: ©2020 Qi et al.
attribution name: Qi et al.

No island-effect on glucocorticoid levels for a rodent from a near-shore archipelago
type: item
type: AcademicArticle
description: Island rodents are often larger and live at higher population densities than their mainland counterparts, characteristics that have been referred to as “island syndrome”. Island syndrome has been well studied, but few studies have tested for island-mainland differences in stress physiology. We evaluated island syndrome within the context of stress physiology of white-footed mice (Peromyscus leucopus) captured from 11 islands and five mainland sites in Thousand Islands National Park, Ontario, Canada. Stress physiology was evaluated by quantifying corticosterone (a stress biomarker), the primary glucocorticoid in mice, from hair and its related metabolites from fecal samples. White-footed mice captured in this near-shore archipelago did not display characteristics of island syndrome, nor differences in levels of hair corticosterone or fecal corticosterone metabolites compared with mainland mice. We suggest that island white-footed mice experience similar degrees of stress in the Thousand Islands compared with the mainland. Although we did not find evidence of island syndrome or differences in glucocorticoid levels, we identified relationships between internal (sex, body mass) and external (season) factors and our hormonal indices of stress in white-footed mice.
format: application/pdf
format: text/html
creator: Nathan D. Stewart
creator: Gabriela F. Mastromonaco
creator: Gary Burness
subject: Biogeography
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.8590
publisher: PeerJ Inc.
rights: © 2020 Stewart et al.
abstract: Island rodents are often larger and live at higher population densities than their mainland counterparts, characteristics that have been referred to as “island syndrome”. Island syndrome has been well studied, but few studies have tested for island-mainland differences in stress physiology. We evaluated island syndrome within the context of stress physiology of white-footed mice (Peromyscus leucopus) captured from 11 islands and five mainland sites in Thousand Islands National Park, Ontario, Canada. Stress physiology was evaluated by quantifying corticosterone (a stress biomarker), the primary glucocorticoid in mice, from hair and its related metabolites from fecal samples. White-footed mice captured in this near-shore archipelago did not display characteristics of island syndrome, nor differences in levels of hair corticosterone or fecal corticosterone metabolites compared with mainland mice. We suggest that island white-footed mice experience similar degrees of stress in the Thousand Islands compared with the mainland. Although we did not find evidence of island syndrome or differences in glucocorticoid levels, we identified relationships between internal (sex, body mass) and external (season) factors and our hormonal indices of stress in white-footed mice.
bibliographic citation: Stewart et al. (2020) No island-effect on glucocorticoid levels for a rodent from a near-shore archipelago. PeerJ 8:e8590 https://doi.org/10.7717/peerj.8590
date submitted: 2019-06-24
date accepted: 2020-01-17
issued: 2020-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stewart
  given name: Nathan D.
author list: Agent
  family name: Mastromonaco
  given name: Gabriela F.
author list: Agent
  family name: Burness
  given name: Gary
doi: 10.7717/peerj.8590
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-18
copyright: ©2020 Stewart et al.
attribution name: Stewart et al.

Effectiveness of slightly acidic electrolyzed water on bacteria reduction: in vitro and spray evaluation
type: item
type: AcademicArticle
description: Bacterial inactivation is a crucial aspect of sanitation and hygiene. The effectiveness of slightly acidic electrolyzed water (SAEW) for reduction or removal of Escherichia coli, Pseudomonas aeruginosa and Staphylococcus epidermidis was evaluated. The bactericidal activity of SAEW and sodium hypochlorite (NaOCl) against E. coli and P. aeruginosa were compared through in vitro experiments. The effectiveness of SAEW spray was tested against S. epidermidis. Results showed that SAEW had a more powerful bactericidal activity than NaOCl at the same available chlorine concentrations. For E. coli, SAEW decreased the bacterial counts from 8.4 log10 CFU/mL to less than 3.9 log10 CFU/mL; NaOCl with the same available chlorine of 0.5 mg/L, caused a decrease from 8.4 log10 CFU/mL to 7.1 log10 CFU/mL. For P. aeruginosa, SAEW caused bacterial counts to decrease from 8.5 log10 CFU/mL to less than 4.1 log10 CFU/mL against 8.5 log10 CFU/mL to 6.2 log10 CFU/mL for NaOCl with the same available chlorine of 0.5 mg/L. Spray experiments showed that 10 mg/L of SAEW spray decreased the bacterial counts of S. epidermidis from 3.7 log10 CFU/m3 to 2.8 log10 CFU/m3, with 20 mg/L causing a reduction from 3.8 log10 CFU/m3 to 0 CFU/m3. The overall findings of this study indicate that SAEW may be a promising disinfectant agent either as a solution or spray.
format: application/pdf
format: text/html
creator: Angelica Naka
creator: Masaya Yakubo
creator: Kenji Nakamura
creator: Midori Kurahashi
subject: Agricultural Science
subject: Food Science and Technology
subject: Microbiology
subject: Public Health
description: doi:10.7717/peerj.8593
publisher: PeerJ Inc.
rights: © 2020 Naka et al.
abstract: Bacterial inactivation is a crucial aspect of sanitation and hygiene. The effectiveness of slightly acidic electrolyzed water (SAEW) for reduction or removal of Escherichia coli, Pseudomonas aeruginosa and Staphylococcus epidermidis was evaluated. The bactericidal activity of SAEW and sodium hypochlorite (NaOCl) against E. coli and P. aeruginosa were compared through in vitro experiments. The effectiveness of SAEW spray was tested against S. epidermidis. Results showed that SAEW had a more powerful bactericidal activity than NaOCl at the same available chlorine concentrations. For E. coli, SAEW decreased the bacterial counts from 8.4 log10 CFU/mL to less than 3.9 log10 CFU/mL; NaOCl with the same available chlorine of 0.5 mg/L, caused a decrease from 8.4 log10 CFU/mL to 7.1 log10 CFU/mL. For P. aeruginosa, SAEW caused bacterial counts to decrease from 8.5 log10 CFU/mL to less than 4.1 log10 CFU/mL against 8.5 log10 CFU/mL to 6.2 log10 CFU/mL for NaOCl with the same available chlorine of 0.5 mg/L. Spray experiments showed that 10 mg/L of SAEW spray decreased the bacterial counts of S. epidermidis from 3.7 log10 CFU/m3 to 2.8 log10 CFU/m3, with 20 mg/L causing a reduction from 3.8 log10 CFU/m3 to 0 CFU/m3. The overall findings of this study indicate that SAEW may be a promising disinfectant agent either as a solution or spray.
bibliographic citation: Naka et al. (2020) Effectiveness of slightly acidic electrolyzed water on bacteria reduction: in vitro and spray evaluation. PeerJ 8:e8593 https://doi.org/10.7717/peerj.8593
date submitted: 2019-10-31
date accepted: 2020-01-18
issued: 2020-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Naka
  given name: Angelica
author list: Agent
  family name: Yakubo
  given name: Masaya
author list: Agent
  family name: Nakamura
  given name: Kenji
author list: Agent
  family name: Kurahashi
  given name: Midori
doi: 10.7717/peerj.8593
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-18
copyright: © 2020 Naka et al.
attribution name: Naka et al.

Fasciola gigantica, F. hepatica and Fasciola intermediate forms: geometric morphometrics and an artificial neural network to help morphological identification
type: item
type: AcademicArticle
description: Background Fasciola hepatica and F. gigantica cause fascioliasis in both humans and livestock. Some adult specimens of Fasciola sp. referred to as “intermediate forms” based on their genetic traits, are also frequently reported. Simple morphological criteria are unreliable for their specific identification. In previous studies, promising phenotypic identification scores were obtained using morphometrics based on linear measurements (distances, angles, curves) between anatomical features. Such an approach is commonly termed “traditional” morphometrics, as opposed to “modern” morphometrics, which is based on the coordinates of anatomical points. Methods Here, we explored the possible improvements that modern methods of morphometrics, including landmark-based and outline-based approaches, could bring to solving the problem of the non-molecular identification of these parasites. F. gigantica and Fasciola intermediate forms suitable for morphometric characterization were selected from Thai strains following their molecular identification. Specimens of F. hepatica were obtained from the Liverpool School of Tropical Medicine (UK). Using these three taxa, we tested the taxonomic signal embedded in traditional linear measurements versus the coordinates of anatomical points (landmark- and outline-based approaches). Various statistical techniques of validated reclassification were used, based on either the shortest Mahalanobis distance, the maximum likelihood, or the artificial neural network method. Results Our results revealed that both traditional and modern morphometric approaches can help in the morphological identification of Fasciola sp. We showed that the accuracy of the traditional approach could be improved by selecting a subset of characters among the most contributive ones. The influence of size on discrimination by shape was much more important in traditional than in modern analyses. In our study, the modern approach provided different results according to the typ…
format: application/pdf
format: text/html
creator: Suchada Sumruayphol
creator: Praphaiphat Siribat
creator: Jean-Pierre Dujardin
creator: Sébastien Dujardin
creator: Chalit Komalamisra
creator: Urusa Thaenkham
subject: Mathematical Biology
subject: Parasitology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.8597
publisher: PeerJ Inc.
rights: © 2020 Sumruayphol et al.
abstract: Background Fasciola hepatica and F. gigantica cause fascioliasis in both humans and livestock. Some adult specimens of Fasciola sp. referred to as “intermediate forms” based on their genetic traits, are also frequently reported. Simple morphological criteria are unreliable for their specific identification. In previous studies, promising phenotypic identification scores were obtained using morphometrics based on linear measurements (distances, angles, curves) between anatomical features. Such an approach is commonly termed “traditional” morphometrics, as opposed to “modern” morphometrics, which is based on the coordinates of anatomical points. Methods Here, we explored the possible improvements that modern methods of morphometrics, including landmark-based and outline-based approaches, could bring to solving the problem of the non-molecular identification of these parasites. F. gigantica and Fasciola intermediate forms suitable for morphometric characterization were selected from Thai strains following their molecular identification. Specimens of F. hepatica were obtained from the Liverpool School of Tropical Medicine (UK). Using these three taxa, we tested the taxonomic signal embedded in traditional linear measurements versus the coordinates of anatomical points (landmark- and outline-based approaches). Various statistical techniques of validated reclassification were used, based on either the shortest Mahalanobis distance, the maximum likelihood, or the artificial neural network method. Results Our results revealed that both traditional and modern morphometric approaches can help in the morphological identification of Fasciola sp. We showed that the accuracy of the traditional approach could be improved by selecting a subset of characters among the most contributive ones. The influence of size on discrimination by shape was much more important in traditional than in modern analyses. In our study, the modern approach provided different results according to the typ…
bibliographic citation: Sumruayphol et al. (2020) Fasciola gigantica, F. hepatica and Fasciola intermediate forms: geometric morphometrics and an artificial neural network to help morphological identification. PeerJ 8:e8597 https://doi.org/10.7717/peerj.8597
date submitted: 2019-08-08
date accepted: 2020-01-18
issued: 2020-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sumruayphol
  given name: Suchada
author list: Agent
  family name: Siribat
  given name: Praphaiphat
author list: Agent
  family name: Dujardin
  given name: Jean-Pierre
author list: Agent
  family name: Dujardin
  given name: Sébastien
author list: Agent
  family name: Komalamisra
  given name: Chalit
author list: Agent
  family name: Thaenkham
  given name: Urusa
doi: 10.7717/peerj.8597
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-18
copyright: ©2020 Sumruayphol et al.
attribution name: Sumruayphol et al.

Injuries among adolescents in Greenland: behavioural and socio-economic correlates among a nationally representative sample
type: item
type: AcademicArticle
description: Background Injuries are among the most important threats to adolescent health, making examination of the patterns and risk factors a critical area of research. There exists a paucity of information on the health and injury experience of school-attending adolescents in Greenland. Consenting Greenlandic schoolchildren (n = 2,254) aged 9–19 years were included in the Health Behavior in School-Aged Children study 2005/2006. The aim of this study was to examine the socio-economic and behavioural correlates that were associated with injury occurrence among school-attending Greenlandic adolescents. Methods This study made use of two multinomial regression models to examine injury occurrence regarding potential influencing factors such as physical activity, risk behaviours, bullying and family socio-economic status (SES). Results Those self-reporting 1–2 injuries within the recall period were more likely to be male (OR = 1.70; CI [1.39–2.09]), involved in physical fighting (OR = 1.82; CI [1.33–2.47]), bullied (OR = 1.81; CI [1.47–2.24]) and participated in bullying others (OR = 1.53; CI [1.25–1.89]). Those reporting three or more injuries were again mostly male (OR = 2.13; CI [1.44–3.14]), involved in physical fighting at higher rates (OR = 4.47; CI [2.86–7.01]), bullied more often (OR = 2.43; CI [1.65–3.57]) and were more likely to bully others (OR = 1.67; CI [1.13–2.45]). Living without a mother proved to be significantly correlated with suffering 3 or more injuries during the recall period (OR = 1.63; CI [1.05–2.52]). The study results support the idea that factors that were found to be associated with injury occurrence, such as bullying and aggressive behaviour, should be taken into account when conducting future research on the nature of injuries among Greenlandic adolescents. More research on this topic is needed to identify factors that might modify the associations between injuries and adolescent behaviour and SES.
format: application/pdf
format: text/html
creator: Louis Jansen
creator: Till Bärnighausen
creator: Michael Lowery Wilson
subject: Global Health
subject: Public Health
description: doi:10.7717/peerj.8605
publisher: PeerJ Inc.
rights: © 2020 Jansen et al.
abstract: Background Injuries are among the most important threats to adolescent health, making examination of the patterns and risk factors a critical area of research. There exists a paucity of information on the health and injury experience of school-attending adolescents in Greenland. Consenting Greenlandic schoolchildren (n = 2,254) aged 9–19 years were included in the Health Behavior in School-Aged Children study 2005/2006. The aim of this study was to examine the socio-economic and behavioural correlates that were associated with injury occurrence among school-attending Greenlandic adolescents. Methods This study made use of two multinomial regression models to examine injury occurrence regarding potential influencing factors such as physical activity, risk behaviours, bullying and family socio-economic status (SES). Results Those self-reporting 1–2 injuries within the recall period were more likely to be male (OR = 1.70; CI [1.39–2.09]), involved in physical fighting (OR = 1.82; CI [1.33–2.47]), bullied (OR = 1.81; CI [1.47–2.24]) and participated in bullying others (OR = 1.53; CI [1.25–1.89]). Those reporting three or more injuries were again mostly male (OR = 2.13; CI [1.44–3.14]), involved in physical fighting at higher rates (OR = 4.47; CI [2.86–7.01]), bullied more often (OR = 2.43; CI [1.65–3.57]) and were more likely to bully others (OR = 1.67; CI [1.13–2.45]). Living without a mother proved to be significantly correlated with suffering 3 or more injuries during the recall period (OR = 1.63; CI [1.05–2.52]). The study results support the idea that factors that were found to be associated with injury occurrence, such as bullying and aggressive behaviour, should be taken into account when conducting future research on the nature of injuries among Greenlandic adolescents. More research on this topic is needed to identify factors that might modify the associations between injuries and adolescent behaviour and SES.
bibliographic citation: Jansen et al. (2020) Injuries among adolescents in Greenland: behavioural and socio-economic correlates among a nationally representative sample. PeerJ 8:e8605 https://doi.org/10.7717/peerj.8605
date submitted: 2019-08-07
date accepted: 2020-01-20
issued: 2020-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jansen
  given name: Louis
author list: Agent
  family name: Bärnighausen
  given name: Till
author list: Agent
  family name: Lowery Wilson
  given name: Michael
doi: 10.7717/peerj.8605
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-18
copyright: © 2020 Jansen et al.
attribution name: Jansen et al.

Co-expression network analysis reveals the pivotal role of mitochondrial dysfunction and interferon signature in juvenile dermatomyositis
type: item
type: AcademicArticle
description: Background Juvenile dermatomyositis (JDM) is an immune-mediated disease characterized by chronic organ inflammation. The pathogenic mechanisms remain ill-defined. Methods Raw microarray data of JDM were obtained from the gene expression omnibus (GEO) database. Based on the GSE3307 dataset with 39 samples, weighted correlation network analysis (WGCNA) was performed to identify key modules associated with pathological state. Functional enrichment analyses were conducted to identify potential mechanisms. Based on the criteria of high connectivity and module membership, candidate hub genes were selected. A protein-protein interaction network was constructed to identify hub genes. Another dataset (GSE11971) was used for the validation of real hub genes. Finally, the real hub genes were used to screen out small-molecule compounds via the Connectivity map database. Results Three modules were considered as key modules for the pathological state of JDM. Functional enrichment analysis indicated that responses to interferon and metabolism were dysregulated. A total of 45 candidate hub genes were selected according to the pre-established criteria, and 20 genes could differentiate JDM from normal controls by validation of another external dataset (GSE11971). These real hub genes suggested the pivotal role of mitochondrial dysfunction and interferon signature in JDM. Furthermore, drug repositioning highlighted the importance of acacetin, helveticoside, lanatoside C, deferoxamine, LY-294002, tanespimycin and L01AD from downregulated genes with the potential to perturb the development of JDM, while betonicine, felodipine, valproic acid, trichostatin A and sirolimus from upregulated genes provided potentially therapeutic goals for JDM. Conclusions There are 20 real hub genes associated with the pathological state of JDM, suggesting the pivotal role of mitochondrial dysfunction and interferon signature in JDM. This analysis predicted several kinds of small-molecule compounds to treat…
format: application/pdf
format: text/html
creator: Danli Zhong
creator: Chanyuan Wu
creator: Jingjing Bai
creator: Dong Xu
creator: Xiaofeng Zeng
creator: Qian Wang
subject: Bioinformatics
subject: Dermatology
subject: Internal Medicine
subject: Rheumatology
subject: Statistics
description: doi:10.7717/peerj.8611
publisher: PeerJ Inc.
rights: © 2020 Zhong et al.
abstract: Background Juvenile dermatomyositis (JDM) is an immune-mediated disease characterized by chronic organ inflammation. The pathogenic mechanisms remain ill-defined. Methods Raw microarray data of JDM were obtained from the gene expression omnibus (GEO) database. Based on the GSE3307 dataset with 39 samples, weighted correlation network analysis (WGCNA) was performed to identify key modules associated with pathological state. Functional enrichment analyses were conducted to identify potential mechanisms. Based on the criteria of high connectivity and module membership, candidate hub genes were selected. A protein-protein interaction network was constructed to identify hub genes. Another dataset (GSE11971) was used for the validation of real hub genes. Finally, the real hub genes were used to screen out small-molecule compounds via the Connectivity map database. Results Three modules were considered as key modules for the pathological state of JDM. Functional enrichment analysis indicated that responses to interferon and metabolism were dysregulated. A total of 45 candidate hub genes were selected according to the pre-established criteria, and 20 genes could differentiate JDM from normal controls by validation of another external dataset (GSE11971). These real hub genes suggested the pivotal role of mitochondrial dysfunction and interferon signature in JDM. Furthermore, drug repositioning highlighted the importance of acacetin, helveticoside, lanatoside C, deferoxamine, LY-294002, tanespimycin and L01AD from downregulated genes with the potential to perturb the development of JDM, while betonicine, felodipine, valproic acid, trichostatin A and sirolimus from upregulated genes provided potentially therapeutic goals for JDM. Conclusions There are 20 real hub genes associated with the pathological state of JDM, suggesting the pivotal role of mitochondrial dysfunction and interferon signature in JDM. This analysis predicted several kinds of small-molecule compounds to treat…
bibliographic citation: Zhong et al. (2020) Co-expression network analysis reveals the pivotal role of mitochondrial dysfunction and interferon signature in juvenile dermatomyositis. PeerJ 8:e8611 https://doi.org/10.7717/peerj.8611
date submitted: 2019-10-22
date accepted: 2020-01-21
issued: 2020-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhong
  given name: Danli
author list: Agent
  family name: Wu
  given name: Chanyuan
author list: Agent
  family name: Bai
  given name: Jingjing
author list: Agent
  family name: Xu
  given name: Dong
author list: Agent
  family name: Zeng
  given name: Xiaofeng
author list: Agent
  family name: Wang
  given name: Qian
doi: 10.7717/peerj.8611
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-18
copyright: ©2020 Zhong et al.
attribution name: Zhong et al.

Association between 9-minute walk/run test and obesity among children and adolescents: evidence for criterion-referenced cut-points
type: item
type: AcademicArticle
description: Background Criterion-referenced cut-points for field-based aerobic fitness for children and adolescents are lacking. This study aimed to determine the associations between aerobic fitness and obesity to propose criterion-referenced cut-points for boys and girls (6–17 years). Methods A total of 61,465 children and adolescents aged 11.2 ± 2.0 years were recruited from 27 sites (all 26 states and Federal District) across Brazil. Aerobic fitness was assessed using 9-min walk/run test reported as distance attained during the test. Body mass index was calculated from measured height and weight and was used to identify obesity. Results The distance covered in the 9-min walk/run test (area under curve > 0.65) had satisfactory predictive ability for obesity. Sensitivity and specificity were moderate (>60%) to strong (>70%) for all age- and sex-specific cut-points. For boys, the optimal physical performance cut-points were, approximately, 1,200 m from 6 to 8 years, 1,300 m from 9 to 11 years, 1,380 m from 12 to 14 years, 1,520 m from 15 to 17 years. For girls, the best cut-points were, approximately, 1,070 m from 6 to 8 years, 1,160 m from 9 to 11 years and 1,200 m from 12 to 17 years. Conclusions The 9-min walk/run test had satisfactory predictive ability for obesity in children and adolescents. The physical fitness cut-points proposed in the present study varied according to age and sex and could be useful and practical tools to identify low levels of physical fitness in children and adolescents in Brazil.
format: application/pdf
format: text/html
creator: Diego Augusto Santos Silva
creator: Justin J. Lang
creator: Edio L. Petroski
creator: Júlio B. Mello
creator: Adroaldo C.A. Gaya
creator: Mark S. Tremblay
subject: Kinesiology
subject: Nutrition
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.8651
publisher: PeerJ Inc.
rights: © 2020 Silva et al.
abstract: Background Criterion-referenced cut-points for field-based aerobic fitness for children and adolescents are lacking. This study aimed to determine the associations between aerobic fitness and obesity to propose criterion-referenced cut-points for boys and girls (6–17 years). Methods A total of 61,465 children and adolescents aged 11.2 ± 2.0 years were recruited from 27 sites (all 26 states and Federal District) across Brazil. Aerobic fitness was assessed using 9-min walk/run test reported as distance attained during the test. Body mass index was calculated from measured height and weight and was used to identify obesity. Results The distance covered in the 9-min walk/run test (area under curve > 0.65) had satisfactory predictive ability for obesity. Sensitivity and specificity were moderate (>60%) to strong (>70%) for all age- and sex-specific cut-points. For boys, the optimal physical performance cut-points were, approximately, 1,200 m from 6 to 8 years, 1,300 m from 9 to 11 years, 1,380 m from 12 to 14 years, 1,520 m from 15 to 17 years. For girls, the best cut-points were, approximately, 1,070 m from 6 to 8 years, 1,160 m from 9 to 11 years and 1,200 m from 12 to 17 years. Conclusions The 9-min walk/run test had satisfactory predictive ability for obesity in children and adolescents. The physical fitness cut-points proposed in the present study varied according to age and sex and could be useful and practical tools to identify low levels of physical fitness in children and adolescents in Brazil.
bibliographic citation: Silva et al. (2020) Association between 9-minute walk/run test and obesity among children and adolescents: evidence for criterion-referenced cut-points. PeerJ 8:e8651 https://doi.org/10.7717/peerj.8651
date submitted: 2019-11-12
date accepted: 2020-01-28
issued: 2020-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva
  given name: Diego Augusto Santos
author list: Agent
  family name: Lang
  given name: Justin J.
author list: Agent
  family name: Petroski
  given name: Edio L.
author list: Agent
  family name: Mello
  given name: Júlio B.
author list: Agent
  family name: Gaya
  given name: Adroaldo C.A.
author list: Agent
  family name: Tremblay
  given name: Mark S.
doi: 10.7717/peerj.8651
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-18
copyright: © 2020 Silva et al.
attribution name: Silva et al.

Molecular phylogeny and intraspecific differentiation of the Trapelus agilis species complex in Iran (Squamata: Agamidae) inferred from mitochondrial DNA sequences
type: item
type: AcademicArticle
description: Background Trapelus agilis consists of different morphotypes with restricted distributions in the Iranian Plateau. The phylogeny of the species complex has not been resolved so far, but recently Trapelus sanguinolentus were elevated from this complex into a full species. Other populations of the species complex need to be evaluated taxonomically. Methods In the present study, several populations of this species complex along with specimens of its closely related taxa in Iran, T. sanguinolentus, T. ruderatus and T. persicus, were examined using partial nucleotide sequences of two mitochondrial genes (cytb and ND2) (total length 1,322 bp). Result Populations of T. sanguinolentus clustered within the T. agilis species complex, thus indicating its paraphyly, but T. sanguinolentus was previously determined to be a species based on morphological features. The T. agilis species complex forms two distinct major clades, each of which is represented by several local populations on the Iranian Plateau. At least five distinct taxa can be identified within this traditional group. Our biogeographic evaluation of the molecular dataset suggested that the Trapelus complex originated in the Late Oligocene (30 mya) and subsequently diversified during the early to middle Miocene (22–13 mya). At first, the predominantly western clade of Trapelus ruderatus diverged from the other clades (22 mya). Afterward, Trapelus persicus diverged around 18 mya ago. The broader T. agilis complex started to diverge about 16 mya, forming several clades on the Iranian Plateau and in Central Asia. The different lineages within this species complex appear to be the result of vicariance events and dispersal waives. The corresponding vicariance events are the formation of the Zagros and Kopet Dagh basins (16–14 mya), and consequently, the aridification of the Iranian Plateau in the late Miocene (11–6 Mya).
format: application/pdf
format: text/html
creator: Ali-Asghar Shahamat
creator: Eskandar Rastegarpouyani
creator: Nasrullah Rastegar-Pouyani
creator: Seyyed Saeed Hosseinian Yousefkhani
creator: Michael Wink
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.8295
publisher: PeerJ Inc.
rights: © 2020 Shahamat et al.
abstract: Background Trapelus agilis consists of different morphotypes with restricted distributions in the Iranian Plateau. The phylogeny of the species complex has not been resolved so far, but recently Trapelus sanguinolentus were elevated from this complex into a full species. Other populations of the species complex need to be evaluated taxonomically. Methods In the present study, several populations of this species complex along with specimens of its closely related taxa in Iran, T. sanguinolentus, T. ruderatus and T. persicus, were examined using partial nucleotide sequences of two mitochondrial genes (cytb and ND2) (total length 1,322 bp). Result Populations of T. sanguinolentus clustered within the T. agilis species complex, thus indicating its paraphyly, but T. sanguinolentus was previously determined to be a species based on morphological features. The T. agilis species complex forms two distinct major clades, each of which is represented by several local populations on the Iranian Plateau. At least five distinct taxa can be identified within this traditional group. Our biogeographic evaluation of the molecular dataset suggested that the Trapelus complex originated in the Late Oligocene (30 mya) and subsequently diversified during the early to middle Miocene (22–13 mya). At first, the predominantly western clade of Trapelus ruderatus diverged from the other clades (22 mya). Afterward, Trapelus persicus diverged around 18 mya ago. The broader T. agilis complex started to diverge about 16 mya, forming several clades on the Iranian Plateau and in Central Asia. The different lineages within this species complex appear to be the result of vicariance events and dispersal waives. The corresponding vicariance events are the formation of the Zagros and Kopet Dagh basins (16–14 mya), and consequently, the aridification of the Iranian Plateau in the late Miocene (11–6 Mya).
bibliographic citation: Shahamat et al. (2020) Molecular phylogeny and intraspecific differentiation of the Trapelus agilis species complex in Iran (Squamata: Agamidae) inferred from mitochondrial DNA sequences. PeerJ 8:e8295 https://doi.org/10.7717/peerj.8295
date submitted: 2019-05-14
date accepted: 2019-11-25
issued: 2020-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shahamat
  given name: Ali-Asghar
author list: Agent
  family name: Rastegarpouyani
  given name: Eskandar
author list: Agent
  family name: Rastegar-Pouyani
  given name: Nasrullah
author list: Agent
  family name: Hosseinian Yousefkhani
  given name: Seyyed Saeed
author list: Agent
  family name: Wink
  given name: Michael
doi: 10.7717/peerj.8295
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-17
copyright: ©2020 Shahamat et al.
attribution name: Shahamat et al.

Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon
type: item
type: AcademicArticle
description: The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and stress responses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon–intron structure. Synteny analysis indicated the presence of a large number of syntenic relationship events between watermelon and cucumber. In promoter analysis, five kinds of stress-related and nine kinds of hormone-related cis-elements were identified in the promoter regions of ClDof genes. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of 12 selected ClDof genes under salt stress and ABA treatments using qRT-PCR. As a result, they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.
format: application/pdf
format: text/html
creator: Yong Zhou
creator: Yuan Cheng
creator: Chunpeng Wan
creator: Jingwen Li
creator: Youxin Yang
creator: Jinyin Chen
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.8358
publisher: PeerJ Inc.
rights: © 2020 Zhou et al.
abstract: The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and stress responses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon–intron structure. Synteny analysis indicated the presence of a large number of syntenic relationship events between watermelon and cucumber. In promoter analysis, five kinds of stress-related and nine kinds of hormone-related cis-elements were identified in the promoter regions of ClDof genes. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of 12 selected ClDof genes under salt stress and ABA treatments using qRT-PCR. As a result, they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.
bibliographic citation: Zhou et al. (2020) Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon. PeerJ 8:e8358 https://doi.org/10.7717/peerj.8358
date submitted: 2019-06-23
date accepted: 2019-12-04
issued: 2020-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Yong
author list: Agent
  family name: Cheng
  given name: Yuan
author list: Agent
  family name: Wan
  given name: Chunpeng
author list: Agent
  family name: Li
  given name: Jingwen
author list: Agent
  family name: Yang
  given name: Youxin
author list: Agent
  family name: Chen
  given name: Jinyin
doi: 10.7717/peerj.8358
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-02-17
copyright: © 2020 Zhou et al.
attribution name: Zhou et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359